State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Sci China Life Sci. 2020 Nov;63(11):1688-1702. doi: 10.1007/s11427-019-1682-6. Epub 2020 Apr 15.
Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.
对大型自然群体进行基因分型和表型分析为群体基因组分析和全基因组关联研究（GWAS）提供了机会。在过去的十年中，已经对几个水稻群体进行了重测序；然而，这些研究并未包括许多中国主要的水稻品种。在这里，我们报告了一个主要由 1275 份来自中国的广泛种植品种和杂交水稻亲本的水稻材料组成的大型基因组和表型数据集。该群体分为三个籼稻/感病和三个粳稻/抗病的进化分支，这与它们的地理或育种起源密切相关。我们共获得了来自不同亚群的 29 个农艺性状在多个环境下的 146 个表型数据集。通过 GWAS，我们总共鉴定到 143 个显著关联位点，其中包括三个新鉴定的控制抽穗期或直链淀粉含量的候选基因或等位基因。我们对群体中农艺重要基因的基因型分析表明，许多有利等位基因在优良品种中未得到充分利用，这表明它们可能被用于未来的育种工作中。我们的研究为水稻遗传研究和育种提供了有用的资源。
